extrProtPSSM: Compute PSSM (Position-Specific Scoring Matrix) for given...
In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence

extrProtPSSM(seq, start.pos = 1L, end.pos = nchar(seq),
  psiblast.path = NULL, makeblastdb.path = NULL,
  database.path = NULL, iter = 5, silent = TRUE, evalue = 10L,
  word.size = NULL, gapopen = NULL, gapextend = NULL,
  matrix = "BLOSUM62", threshold = NULL, seg = "no",
  soft.masking = FALSE, culling.limit = NULL,
  best.hit.overhang = NULL, best.hit.score.edge = NULL,
  xdrop.ungap = NULL, xdrop.gap = NULL, xdrop.gap.final = NULL,
  window.size = NULL, gap.trigger = 22L, num.threads = 1L,
  pseudocount = 0L, inclusion.ethresh = 0.002)

`seq`	Character vector, as the input protein sequence.
`start.pos`	Optional integer denoting the start position of the fragment window. Default is `1`, i.e. the first amino acid of the given sequence.
`end.pos`	Optional integer denoting the end position of the fragment window. Default is `nchar(seq)`, i.e. the last amino acid of the given sequence.
`psiblast.path`	Character string indicating the path of the `psiblast` program. If NCBI Blast+ was previously installed in the operation system, the path will be automatically detected.
`makeblastdb.path`	Character string indicating the path of the `makeblastdb` program. If NCBI Blast+ was previously installed in the system, the path will be automatically detected.
`database.path`	Character string indicating the path of a reference database (a FASTA file).
`iter`	Number of iterations to perform for PSI-Blast.
`silent`	Logical. Whether the PSI-Blast running output should be shown or not (May not work on some Windows versions and PSI-Blast versions), default is `TRUE`.
`evalue`	Expectation value (E) threshold for saving hits. Default is `10`.
`word.size`	Word size for wordfinder algorithm. An integer >= 2.
`gapopen`	Integer. Cost to open a gap.
`gapextend`	Integer. Cost to extend a gap.
`matrix`	Character string. The scoring matrix name (default is `'BLOSUM62'`).
`threshold`	Minimum word score such that the word is added to the BLAST lookup table. A real value >= 0.
`seg`	Character string. Filter query sequence with SEG (`'yes'`, `'window locut hicut'`, or `'no'` to disable) Default is `'no'`.
`soft.masking`	Logical. Apply filtering locations as soft masks? Default is `FALSE`.
`culling.limit`	An integer >= 0. If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit. Incompatible with `best.hit.overhang` and `best_hit_score_edge`.
`best.hit.overhang`	Best Hit algorithm overhang value (A real value >= 0 and =< 0.5, recommended value: 0.1). Incompatible with `culling_limit`.
`best.hit.score.edge`	Best Hit algorithm score edge value (A real value >=0 and =< 0.5, recommended value: 0.1). Incompatible with `culling_limit`.
`xdrop.ungap`	X-dropoff value (in bits) for ungapped extensions.
`xdrop.gap`	X-dropoff value (in bits) for preliminary gapped extensions.
`xdrop.gap.final`	X-dropoff value (in bits) for final gapped alignment.
`window.size`	An integer >= 0. Multiple hits window size, To specify 1-hit algorithm, use `0`.
`gap.trigger`	Number of bits to trigger gapping. Default is `22`.
`num.threads`	Integer. Number of threads (CPUs) to use in the BLAST search. Default is `1`.
`pseudocount`	Integer. Pseudo-count value used when constructing PSSM. Default is `0`.
`inclusion.ethresh`	E-value inclusion threshold for pairwise alignments. Default is `0.002`.

This function calculates the PSSM (Position-Specific Scoring Matrix) derived by PSI-Blast for given protein sequence or peptides. For given protein sequences or peptides, PSSM represents the log-likelihood of the substitution of the 20 types of amino acids at that position in the sequence. Note that the output value is not normalized.

The original PSSM, a numeric matrix which has end.pos - start.pos + 1 columns and 20 named rows.

The function requires the makeblastdb and psiblast programs to be properly installed in the operation system or their paths provided.

The two command-line programs are included in the NCBI-BLAST+ software package. To install NCBI Blast+, just open the NCBI FTP site using web browser or FTP software: ftp://anonymous@ftp.ncbi.nlm.nih.gov:21/blast/executables/blast+/LATEST/ then download the executable version of BLAST+ according to your operation system, and compile or install the downloaded source code or executable program.

Ubuntu/Debian users can directly use the command sudo apt-get install ncbi-blast+ to install NCBI Blast+. For OS X users, download ncbi-blast- ... .dmg then install. For Windows users, download ncbi-blast- ... .exe then install.

Min-feng Zhu <wind2zhu@163.com>, Nan Xiao <http://r2s.name>

Altschul, Stephen F., et al. "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic acids research 25.17 (1997): 3389–3402.

Ye, Xugang, Guoli Wang, and Stephen F. Altschul. "An assessment of substitution scores for protein profile-profile comparison." Bioinformatics 27.24 (2011): 3356–3363.

Rangwala, Huzefa, and George Karypis. "Profile-based direct kernels for remote homology detection and fold recognition." Bioinformatics 21.23 (2005): 4239–4247.

extrProtPSSMFeature extrProtPSSMAcc

x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
dbpath = tempfile('tempdb', fileext = '.fasta')
invisible(file.copy(from = system.file('protseq/Plasminogen.fasta', 
package = 'BioMedR'), to = dbpath))
pssmmat = extrProtPSSM(seq = x, database.path = dbpath)
dim(pssmmat)  # 20 x 562 (P00750: length 562, 20 Amino Acids)